Cocrystal Structure of a tRNA Ψ55 Pseudouridine Synthase: Nucleotide Flipping by an RNA-Modifying Enzyme

Pseudouridine (Ψ) synthases catalyze the isomerization of specific uridines in cellular RNAs to pseudouridines and may function as RNA chaperones. TruB is responsible for the Ψ residue present in the T loops of virtually all tRNAs. The close homolog Cbf5/dyskerin is the catalytic subunit of box H/ACA snoRNPs. These carry out the pseudouridylation of eukaryotic rRNA and snRNAs. The 1.85 Å resolution structure of TruB bound to RNA reveals that this enzyme recognizes the preformed three-dimensional structure of the T loop, primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA. Structural comparisons with TruB demonstrate that all Ψ synthases are descended from a common molecular ancestor.